How does a protein search for the specific site on DNA: the role of disorder

Abstract: Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to nonspecific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such a one-dimensional route towards the target an "antenna." We studied the role of the dispersion of nonspecific binding energies within the antenna due to a quasirandom sequence of natural DNA. A random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for macroscopic and mesoscopic antennas.

Cited as: Tao Hu and B.I. Shklovskii, "How does a protein search for the specific site on DNA: the role of disorder", Physical Review E 74, 021903 (2006)